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          <td width="35%" class="headerValue"><a href="../../../../../../../../index.html">directory</a> - <a href="index.html">home/andres/Programacion/aso_coverage/aso/src/ASO/framework</a> - antiviral.h (source / <a href="antiviral.h.func.html">functions</a>)</td>
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          <td width="10%" class="headerCovTableHead">Found</td>
          <td width="10%" class="headerCovTableHead">Hit</td>
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          <td class="headerValue">cover.info</td>
          <td class="headerItem">Lines:</td>
          <td class="headerCovTableEntry">32</td>
          <td class="headerCovTableEntry">28</td>
          <td class="headerCovTableEntryHi">87.5 %</td>
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          <td class="headerItem">Date:</td>
          <td class="headerValue">2010-08-03</td>
          <td class="headerItem">Functions:</td>
          <td class="headerCovTableEntry">13</td>
          <td class="headerCovTableEntry">12</td>
          <td class="headerCovTableEntryHi">92.3 %</td>
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      <td><pre class="source">
<a name="1"><span class="lineNum">       1 </span>                : /**</a>
<span class="lineNum">       2 </span>                :  * \file  antiviral.h
<span class="lineNum">       3 </span>                :  * \brief Definition of Antiviral class.
<span class="lineNum">       4 </span>                :  *
<span class="lineNum">       5 </span>                :  * ASO: Antiviral Sequence Optimizer
<span class="lineNum">       6 </span>                :  * &lt;http://aso.googlecode.com/&gt;
<span class="lineNum">       7 </span>                :  * Copyright (C) 2010 Velez Ezequiel, Peralta Andres, FuDePAN
<span class="lineNum">       8 </span>                :  *
<span class="lineNum">       9 </span>                :  * This file is part of the ASO project.
<span class="lineNum">      10 </span>                :  *
<span class="lineNum">      11 </span>                :  * Contents:       Header file for ASO providing class Antiviral.
<span class="lineNum">      12 </span>                :  *
<span class="lineNum">      13 </span>                :  * System:         ASO
<span class="lineNum">      14 </span>                :  * Language:       C++
<span class="lineNum">      15 </span>                :  *
<span class="lineNum">      16 </span>                :  * Author:         Velez Ezequiel, Peralta Andres
<span class="lineNum">      17 </span>                :  * E-Mail:
<span class="lineNum">      18 </span>                :  *
<span class="lineNum">      19 </span>                :  * ASO is free software: you can redistribute it and/or modify
<span class="lineNum">      20 </span>                :  * it under the terms of the GNU General Public License as published by
<span class="lineNum">      21 </span>                :  * the Free Software Foundation, either version 3 of the License, or
<span class="lineNum">      22 </span>                :  * (at your option) any later version.
<span class="lineNum">      23 </span>                :  *
<span class="lineNum">      24 </span>                :  * ASO is distributed in the hope that it will be useful,
<span class="lineNum">      25 </span>                :  * but WITHOUT ANY WARRANTY; without even the implied warranty of
<span class="lineNum">      26 </span>                :  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
<span class="lineNum">      27 </span>                :  * GNU General Public License for more details.
<span class="lineNum">      28 </span>                :  *
<span class="lineNum">      29 </span>                :  * You should have received a copy of the GNU General Public License
<span class="lineNum">      30 </span>                :  * along with ASO.  If not, see &lt;http://www.gnu.org/licenses/&gt;.
<span class="lineNum">      31 </span>                :  *
<span class="lineNum">      32 </span>                :  */
<span class="lineNum">      33 </span>                : 
<span class="lineNum">      34 </span>                : #ifndef ANTIVIRAL_H
<span class="lineNum">      35 </span>                : #define ANTIVIRAL_H
<span class="lineNum">      36 </span>                : 
<span class="lineNum">      37 </span>                : #define NO_BITWISE_ENUMS
<span class="lineNum">      38 </span>                : #include &lt;mili/mili.h&gt;
<span class="lineNum">      39 </span>                : #include &quot;sequence.h&quot;
<span class="lineNum">      40 </span>                : 
<span class="lineNum">      41 </span>                : 
<span class="lineNum">      42 </span>                : /*! Lista de tripletes para la aplicacion de las resistencias.*/
<span class="lineNum">      43 </span>                : typedef std::set&lt;Triplet&gt; TripletList;
<span class="lineNum">      44 </span>                : 
<span class="lineNum">      45 </span>                : /*! Valor para las distancias entre mutantes. */
<span class="lineNum">      46 </span>                : typedef float DistanceValue;
<span class="lineNum">      47 </span>                : 
<a name="48"><span class="lineNum">      48 </span>                : /*! Par que guarda las mutantes y la distancia mínima*/</a>
<span class="lineNum">      49 </span>                : struct MutantDist
<span class="lineNum">      50 </span><span class="lineCov">             25 : {</span>
<span class="lineNum">      51 </span>                :     SequenceSet sequences;
<span class="lineNum">      52 </span>                :     DistanceValue distance;
<a name="53"><span class="lineNum">      53 </span>                : </a>
<span class="lineNum">      54 </span>                :     /*! Constructor */
<span class="lineNum">      55 </span><span class="lineCov">             25 :     MutantDist(): sequences(), distance()</span>
<span class="lineNum">      56 </span><span class="lineCov">             25 :     {}</span>
<span class="lineNum">      57 </span>                :     /*! Constructor por copia. */
<span class="lineNum">      58 </span>                :     MutantDist(const SequenceSet&amp; sequences, DistanceValue distance)
<span class="lineNum">      59 </span>                :             : sequences(sequences), distance(distance)
<span class="lineNum">      60 </span>                :     {}
<span class="lineNum">      61 </span>                : };
<span class="lineNum">      62 </span>                : 
<span class="lineNum">      63 </span>                : /*! Par con la lista de tripletes y la distancia mínima.*/
<span class="lineNum">      64 </span>                : typedef std::pair&lt;TripletList, DistanceValue&gt; TripletVal;
<span class="lineNum">      65 </span>                : typedef VariantsSet AttribSet;
<span class="lineNum">      66 </span>                : 
<span class="lineNum">      67 </span>                : /*! Interfaz de Antiviral */
<span class="lineNum">      68 </span>                : class Antiviral
<span class="lineNum">      69 </span>                : {
<span class="lineNum">      70 </span>                :     AttribSet attributes; //! todo el conjunto de atributos    
<span class="lineNum">      71 </span>                : 
<a name="72"><span class="lineNum">      72 </span>                : public:</a>
<span class="lineNum">      73 </span>                :     /*! Constructor */
<span class="lineNum">      74 </span><span class="lineCov">             63 :     Antiviral(const std::string&amp; name)</span>
<span class="lineNum">      75 </span><span class="lineCov">             63 :     {</span>
<span class="lineNum">      76 </span><span class="lineCov">             63 :         attributes.insert(&quot;name&quot;, name);</span>
<span class="lineNum">      77 </span><span class="lineCov">             63 :     }</span>
<a name="78"><span class="lineNum">      78 </span>                : </a>
<span class="lineNum">      79 </span>                :     /*! Constructor de Antiviral */
<span class="lineNum">      80 </span><span class="lineCov">             30 :     Antiviral(const Antiviral&amp; other)</span>
<span class="lineNum">      81 </span><span class="lineCov">             30 :     {</span>
<span class="lineNum">      82 </span><span class="lineCov">             30 :         attributes = other.attributes;</span>
<span class="lineNum">      83 </span><span class="lineCov">             30 :     }</span>
<span class="lineNum">      84 </span>                : 
<a name="85"><span class="lineNum">      85 </span>                :     /*! Set/Reset de un atributo */</a>
<span class="lineNum">      86 </span>                :     template&lt;class T&gt;
<span class="lineNum">      87 </span><span class="lineCov">            192 :     void set_attrib(const std::string&amp; name, const T&amp; initValue)</span>
<span class="lineNum">      88 </span>                :     {
<span class="lineNum">      89 </span><span class="lineCov">            192 :         attributes.insert(name, initValue);</span>
<span class="lineNum">      90 </span><span class="lineCov">            192 :     }</span>
<span class="lineNum">      91 </span>                : 
<a name="92"><span class="lineNum">      92 </span>                :     /*! Retorna un atributo de acuerdo al nombre */</a>
<span class="lineNum">      93 </span>                :     template&lt;class T&gt;
<span class="lineNum">      94 </span><span class="lineCov">           1701 :     bool get_attrib(const std::string&amp; name, T&amp; value) const throw(SystemError)</span>
<span class="lineNum">      95 </span>                :     {
<span class="lineNum">      96 </span><span class="lineCov">           1701 :         bool found(true);</span>
<span class="lineNum">      97 </span>                :         try
<span class="lineNum">      98 </span>                :         {
<span class="lineNum">      99 </span><span class="lineCov">           1701 :             attributes.get_element(name, value);</span>
<span class="lineNum">     100 </span>                :         }
<span class="lineNum">     101 </span><span class="lineNoCov">              0 :         catch (const BadElementType&amp; exc)</span>
<span class="lineNum">     102 </span>                :         {
<span class="lineNum">     103 </span><span class="lineNoCov">              0 :             throw SystemError(&quot;at Antiviral : Bad Attribute Type&quot;);</span>
<span class="lineNum">     104 </span>                :         }
<span class="lineNum">     105 </span><span class="lineNoCov">              0 :         catch (const BadElementName&amp; exc)</span>
<span class="lineNum">     106 </span>                :         {
<span class="lineNum">     107 </span><span class="lineNoCov">              0 :             found = false;</span>
<span class="lineNum">     108 </span>                :         }
<span class="lineNum">     109 </span><span class="lineCov">           1701 :         return found;</span>
<span class="lineNum">     110 </span>                :     }
<span class="lineNum">     111 </span>                : 
<span class="lineNum">     112 </span>                :     /*! Dada una secuencia, saber si esta aplica a este antiviral */
<span class="lineNum">     113 </span>                :     virtual float applies(const NucSequence&amp; sequence) const = 0;
<span class="lineNum">     114 </span>                : 
<span class="lineNum">     115 </span>                :     /*! Devuelve las mutantes luego de aplicar este antiviral a la secuencia */
<span class="lineNum">     116 </span>                :     virtual void mutate_sequence(const NucSequence&amp; sequence, MutantDist&amp; mutations) const = 0;
<a name="117"><span class="lineNum">     117 </span>                : </a>
<span class="lineNum">     118 </span>                :     /*! Destructor del tipo antiviral */
<span class="lineNum">     119 </span><span class="lineCov">             78 :     ~Antiviral() {};   </span>
<a name="120"><span class="lineNum">     120 </span>                : </a>
<span class="lineNum">     121 </span>                :     /*! Imprime la lista de atributos del antiviral. */
<span class="lineNum">     122 </span><span class="lineCov">             15 :     inline void print_attributes() const</span>
<span class="lineNum">     123 </span>                :     {
<span class="lineNum">     124 </span><span class="lineCov">             15 :         std::string name, value;</span>
<span class="lineNum">     125 </span><span class="lineCov">             15 :         CAutonomousIterator&lt;AttribSet&gt; it(attributes);</span>
<span class="lineNum">     126 </span><span class="lineCov">             93 :         while (!it.end())</span>
<span class="lineNum">     127 </span>                :         {
<span class="lineNum">     128 </span><span class="lineCov">             63 :             get_attrib(it-&gt;first, value);</span>
<span class="lineNum">     129 </span><span class="lineCov">             63 :             std::cout &lt;&lt; it-&gt;first &lt;&lt; &quot;: &quot; &lt;&lt; value &lt;&lt; &quot;.&quot; &lt;&lt; std::endl;</span>
<span class="lineNum">     130 </span><span class="lineCov">             63 :             ++it;</span>
<span class="lineNum">     131 </span><span class="lineCov">             15 :         }</span>
<span class="lineNum">     132 </span><span class="lineCov">             15 :     }</span>
<span class="lineNum">     133 </span>                : 
<span class="lineNum">     134 </span>                : };
<span class="lineNum">     135 </span>                : 
<span class="lineNum">     136 </span>                : #endif
</pre>
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